Contacts of the helix formed by residues 63 - 75 (chain R) in PDB entry 1FKA
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 63 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704A C 5.2 9.1 + - - +
58R LEU 5.8 1.1 - - - +
59R SER* 5.1 13.2 - - - -
60R GLY 4.8 3.4 - - - +
61R LYS 3.7 4.4 + - - +
62R GLU* 1.3 74.4 - - - +
64R ARG* 1.3 56.7 + - - +
65R ILE* 3.2 2.7 - - - +
66R LEU* 3.1 16.7 + - + +
67R ALA* 2.8 33.3 + - - +
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Residues in contact with ARG 64 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A G 3.7 23.6 - - - +
62R GLU* 3.7 6.1 - - + +
63R GLN* 1.3 79.5 - - - +
65R ILE* 1.3 61.6 + - - +
67R ALA* 3.4 19.2 + - - +
68R LYS* 3.6 8.0 + - - +
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Residues in contact with ILE 65 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43R PHE* 4.8 5.4 - - + +
44R LEU* 4.9 8.2 - - + +
62R GLU* 5.4 1.5 - - + +
63R GLN* 3.2 0.6 - - - +
64R ARG* 1.3 79.4 - - - +
66R LEU* 1.3 60.9 + - - +
68R LYS* 3.9 6.5 + - - +
69R THR* 3.6 15.8 + - - -
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Residues in contact with LEU 66 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R PHE* 4.1 23.7 - - + +
62R GLU 5.4 0.4 - - - +
63R GLN* 3.1 22.9 + - + +
65R ILE* 1.3 78.5 - - - +
67R ALA* 1.3 65.7 + - - +
68R LYS 3.2 0.2 - - - -
69R THR* 2.9 24.4 + - - -
70R ILE* 3.0 9.7 + - - +
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Residues in contact with ALA 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704A C 3.9 30.0 - - - +
719A C 5.9 1.1 - - - +
63R GLN 2.8 13.4 + - - +
64R ARG* 3.5 14.8 - - - +
65R ILE 3.4 0.2 - - - -
66R LEU* 1.3 77.1 - - - +
68R LYS* 1.3 63.1 + - - +
70R ILE* 3.5 6.1 + - - +
71R LYS* 3.2 21.1 + - - +
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Residues in contact with LYS 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A C 3.9 16.3 - - - +
720A C 3.5 26.9 + - - +
64R ARG 3.6 7.7 + - - +
65R ILE* 4.1 9.4 - - - +
66R LEU 3.2 0.4 - - - -
67R ALA* 1.3 77.1 - - - +
69R THR* 1.3 55.9 + - - +
71R LYS* 3.3 7.6 + - - +
72R ARG* 2.8 36.4 + - - +
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Residues in contact with THR 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F PHE 4.5 6.5 - - - -
43R PHE 3.3 25.8 - - - -
44R LEU* 3.9 17.7 - - - -
45R SER 5.4 0.9 - - - -
46R GLU* 3.5 10.3 - - - +
65R ILE 3.6 4.7 + - - -
66R LEU 2.9 14.1 + - - -
68R LYS* 1.3 78.4 - - - +
70R ILE* 1.3 64.7 + - - +
72R ARG* 2.9 9.5 + - - +
73R ALA 2.9 18.5 + - - -
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Residues in contact with ILE 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53R ARG 5.0 11.0 - - - +
54R ARG* 5.8 3.8 - - - -
55R ARG 6.2 0.4 - - - +
66R LEU 3.0 7.9 + - - +
67R ALA* 3.9 8.7 - - - +
69R THR* 1.3 77.4 - - - +
71R LYS* 1.3 59.0 + - - +
73R ALA* 3.1 9.0 + - - +
74R ARG* 2.8 29.9 + - - +
78R LEU* 4.6 2.3 - - - +
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Residues in contact with LYS 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A C 5.9 4.9 - - - +
718A G 4.0 20.9 - - - +
719A C 4.0 19.0 + - - +
67R ALA 3.2 12.2 + - - +
68R LYS 3.6 7.2 - - - +
69R THR 3.2 0.4 - - - -
70R ILE* 1.3 79.4 - - - +
72R ARG* 1.3 62.2 + - - +
74R ARG* 3.5 8.6 + - - +
75R ILE* 3.4 19.9 + - - +
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Residues in contact with ARG 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A C 4.6 13.9 + - - +
720A C 5.6 5.6 - - - +
97F PHE 4.9 5.4 - - - +
46R GLU* 4.4 8.7 - - + -
68R LYS 2.8 20.6 + - - +
69R THR* 2.9 8.7 + - - +
71R LYS* 1.3 73.5 - - - +
73R ALA* 1.3 61.1 + - - +
75R ILE* 3.5 18.3 + - - +
76R LEU* 3.8 7.1 + - - +
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Residues in contact with ALA 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46R GLU* 3.6 30.5 - - + +
49R LYS* 5.4 7.4 - - + -
69R THR 2.9 11.0 + - - +
70R ILE* 3.5 11.4 - - - +
72R ARG* 1.3 74.0 - - - +
74R ARG* 1.3 55.3 + - - +
75R ILE 3.0 1.8 - - - -
76R LEU* 2.7 25.2 + - - -
77R GLY 2.8 18.0 + - - -
78R LEU* 3.3 15.3 + - + -
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Residues in contact with ARG 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A G 5.4 1.7 + - - -
49F ALA* 3.3 20.5 - - - +
50F TYR* 6.0 0.3 - - - +
70R ILE 2.8 17.3 + - - +
71R LYS* 3.7 10.5 - - - +
72R ARG 3.4 0.2 - - - -
73R ALA* 1.3 76.4 - - - +
75R ILE* 1.3 60.1 + - - +
78R LEU* 3.4 23.7 - - + +
80R PRO* 4.6 13.4 - - + +
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Residues in contact with ILE 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A G 5.1 24.7 - - - +
718A G 5.2 10.1 - - - +
71R LYS 3.4 10.4 + - - +
72R ARG* 3.5 13.2 - - - +
73R ALA 3.0 0.8 - - - -
74R ARG* 1.3 78.5 - - - +
76R LEU* 1.3 59.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il